From 9a0765939ee6459412f0d1a80c3cad29358d191c Mon Sep 17 00:00:00 2001 From: Xavier Robin <xavier.robin@unibas.ch> Date: Tue, 15 Oct 2024 12:12:59 +0200 Subject: [PATCH] doc: minor improvements for ligand scorer objects --- modules/mol/alg/pymod/ligand_scoring_base.py | 5 +++-- modules/mol/alg/pymod/ligand_scoring_scrmsd.py | 8 ++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/modules/mol/alg/pymod/ligand_scoring_base.py b/modules/mol/alg/pymod/ligand_scoring_base.py index 8710b05d1..86a379fac 100644 --- a/modules/mol/alg/pymod/ligand_scoring_base.py +++ b/modules/mol/alg/pymod/ligand_scoring_base.py @@ -43,9 +43,10 @@ class LigandScorer: * :class:`ost.mol.alg.ligand_scoring_lddtpli.LDDTPLIScorer` that assesses the conservation of protein-ligand - contacts + contacts (lDDT-PLI); * :class:`ost.mol.alg.ligand_scoring_scrmsd.SCRMSDScorer` - that computes a binding-site superposed, symmetry-corrected RMSD. + that computes a binding-site superposed, symmetry-corrected RMSD + (BiSyRMSD) and ligand pocket lDDT (lDDT-LP). All versus all scores are available through the lazily computed :attr:`score_matrix`. However, many things can go wrong... be it even diff --git a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py index 9ae0546d6..345057a7e 100644 --- a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py +++ b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py @@ -8,7 +8,7 @@ from ost.mol.alg import ligand_scoring_base class SCRMSDScorer(ligand_scoring_base.LigandScorer): - """ :class:`LigandScorer` implementing symmetry corrected RMSD. + """ :class:`LigandScorer` implementing symmetry corrected RMSD (BiSyRMSD). :class:`SCRMSDScorer` computes a score for a specific pair of target/model ligands. @@ -33,12 +33,12 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer): faster in case of large complexes. Symmetry correction is achieved by simply computing an RMSD value for each symmetry, i.e. atom-atom assignments of the ligand as given by - :class:`LigandScorer`. The lowest RMSD value is returned + :class:`LigandScorer`. The lowest RMSD value is returned. Populates :attr:`LigandScorer.aux_data` with following :class:`dict` keys: - * rmsd: The score - * lddt_lp: lDDT of the binding site used for superposition + * rmsd: The BiSyRMSD score + * lddt_lp: lDDT of the binding pocket used for superposition * bs_ref_res: :class:`list` of binding site residues in target * bs_ref_res_mapped: :class:`list` of target binding site residues that are mapped to model -- GitLab